ArticleBiophysical journal2010
Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagrams.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 44 citations in OpenAlex.
- Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model.bioRxiv : the preprint server for biology · 2024Article
- Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles.Biophysical journal · 2024Article
- Nucleosome spacing controls chromatin spatial structure and accessibility.Biophysical journal · 2024Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions.Biophysical journal · 2022Article
- Differences in nanoscale organization of regulatory active and inactive human chromatin.Biophysical journal · 2022Article
- How Genomes Emerge, Function, and Evolve: Living Systems Emergence-Genotype-Phenotype-Multilism-Genome/Systems Ecology.Results and problems in cell differentiation · 2022Article
- Simulation of Different Three-Dimensional Models of Whole Interphase Nuclei Compared to Experiments - A Consistent Scale-Bridging Simulation Framework for Genome Organization.Results and problems in cell differentiation · 2022Article
- Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.Nature communications · 2021Article
- Biomolecular modeling thrives in the age of technology.Nature computational science · 2021Article
- Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure.The EMBO journal · 2019Article
- The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes.Epigenetics & chromatin · 2016Article
- Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells.Epigenetics & chromatin · 2016Article
- The chromatin fiber: multiscale problems and approaches.Current opinion in structural biology · 2015Review
- Changing chromatin fiber conformation by nucleosome repositioning.Biophysical journal · 2014Article
- The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes.Journal of the Royal Society, Interface · 2014Article
- Article
- Unwinding and rewinding the nucleosome inner turn: force dependence of the kinetic rate constants.Physical review. E, Statistical, nonlinear, and soft matter physics · 2013Article
- Short nucleosome repeats impose rotational modulations on chromatin fibre folding.The EMBO journal · 2012Article
- Toward convergence of experimental studies and theoretical modeling of the chromatin fiber.The Journal of biological chemistry · 2012Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The three-dimensional structure of chromatin affects DNA accessibility and is therefore a key regulator of gene expression. However, the path of the DNA between consecutive nucleosomes, and the resulting chromatin fiber organization remain controversial. The conformational space available for the folding of the nucleosome chain has been analytically described by phase diagrams with a two-angle model, which describes the chain trajectory by a DNA entry-exit angle at the nucleosome and a torsion angle between consecutive nucleosomes. Here, a novel type of numerical phase diagrams is introduced that relates the geometric phase space to the energy associated with a given chromatin conformation. The resulting phase diagrams revealed differences in the energy landscape that reflect the probability of a given conformation to form in thermal equilibrium. Furthermore, we investigated the effects of entropy and additional degrees of freedom in the dynamic phase diagrams by performing Monte Carlo simulations of the initial chain trajectories. Using our approach, we were able to demonstrate that conformations that initially were geometrically impossible could evolve into energetically favorable states in thermal equilibrium due to DNA bending and torsion. In addition, dynamic phase diagrams were applied to identify chromatin fibers that reflect certain experimentally determined features.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.